FMO DATABASE

FMODB ID: 2N8RR

Calculation Name: 3CNU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CNU

Chain ID: A

ChEMBL ID:

UniProt ID: O28738

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-844433.287399
FMO2-HF: Nuclear repulsion	799478.699733
FMO2-HF: Total energy	-44954.587666
FMO2-MP2: Total energy	-45081.155137

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-18.998	-12.663	17.371	-8.716	-14.99	-0.044

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.012

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	GLU	-1	-0.771	-0.892	3.234	-2.069	0.428	0.088	-1.282	-1.303	0.001
4	A	4	ALA	0	0.006	0.006	5.852	1.051	1.051	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.866	0.941	2.330	-5.342	-6.036	7.926	-2.088	-5.144	0.001
6	A	6	GLU	-1	-0.881	-0.933	3.056	0.781	1.824	0.078	-0.295	-0.827	-0.001
7	A	7	LEU	0	-0.032	-0.015	4.483	0.094	0.217	0.002	-0.021	-0.103	0.000
8	A	8	ILE	0	0.012	0.001	7.238	0.057	0.057	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.812	0.909	2.357	-6.531	-6.749	3.573	-0.889	-2.466	0.006
10	A	10	LYS	1	0.913	0.946	7.020	-1.118	-1.118	0.000	0.000	0.000	0.000
11	A	11	MET	0	-0.018	-0.003	9.684	-0.304	-0.304	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.022	-0.017	9.737	-0.128	-0.128	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.901	-0.954	9.018	1.708	1.708	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.030	-0.004	11.991	-0.181	-0.181	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.020	-0.006	14.836	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.028	-0.033	12.553	-0.154	-0.154	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.087	-0.058	15.825	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.001	0.007	18.095	-0.071	-0.071	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.779	-0.882	20.763	0.231	0.231	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.935	-0.970	23.513	0.197	0.197	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.029	0.009	18.289	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.053	-0.021	20.113	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.780	0.868	22.134	-0.221	-0.221	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.973	-0.975	23.219	0.213	0.213	0.000	0.000	0.000	0.000
25	A	25	MET	0	-0.060	-0.016	17.754	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.019	0.008	22.354	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.068	-0.034	24.798	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	28	TRP	0	-0.021	-0.009	18.910	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.017	-0.028	21.311	0.018	0.018	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.021	0.001	19.982	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.032	-0.009	14.873	0.047	0.047	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.018	0.018	13.989	-0.078	-0.078	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.013	-0.013	10.819	0.182	0.182	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.000	-0.009	9.245	-0.158	-0.158	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.898	0.946	10.224	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.029	-0.015	6.519	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.854	-0.936	8.337	-0.979	-0.979	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.027	-0.011	10.367	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.827	-0.891	2.330	-6.620	-5.119	2.989	-2.349	-2.141	-0.023
40	A	40	GLU	-1	-0.862	-0.929	6.894	0.442	0.442	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.040	-0.040	5.685	0.647	0.647	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.032	-0.008	7.706	-0.313	-0.313	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.026	0.015	9.362	0.295	0.295	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.832	-0.914	11.803	0.455	0.455	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.022	0.000	14.237	0.075	0.075	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.887	0.928	16.804	-0.564	-0.564	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.021	-0.008	20.399	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.852	-0.906	20.910	0.371	0.371	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.052	0.026	21.450	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.077	-0.045	17.089	0.046	0.046	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.058	-0.030	13.797	0.022	0.022	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.840	-0.886	11.633	0.675	0.675	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.061	0.027	4.361	-0.101	0.319	0.014	-0.110	-0.324	0.000
54	A	54	LYS	1	0.754	0.878	7.277	-0.877	-0.877	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.768	-0.890	2.515	0.162	1.825	2.701	-1.682	-2.682	-0.028
56	A	56	GLY	0	-0.011	0.000	5.851	-0.236	-0.236	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.002	-0.005	8.639	0.074	0.074	0.000	0.000	0.000	0.000
58	A	58	HIS	0	0.054	0.040	12.184	-0.042	-0.042	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.012	-0.013	14.659	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.104	-0.063	18.209	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.026	0.032	16.443	0.004	0.004	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.037	-0.022	18.560	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.015	-0.016	17.241	-0.039	-0.039	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.012	0.002	14.533	0.075	0.075	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.005	0.006	13.312	-0.064	-0.064	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.040	-0.025	13.453	0.013	0.013	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.035	0.006	12.659	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.082	0.046	12.095	-0.053	-0.053	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.005	0.014	7.836	0.100	0.100	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.883	-0.947	9.778	-1.353	-1.353	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.000	-0.002	11.989	0.138	0.138	0.000	0.000	0.000	0.000
72	A	72	TRP	0	0.041	0.006	9.490	0.057	0.057	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.042	-0.015	8.803	0.148	0.148	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.020	0.012	11.047	0.113	0.113	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.046	-0.021	14.348	0.076	0.076	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.042	-0.015	9.263	0.064	0.064	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.800	0.894	11.413	0.759	0.759	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.009	0.005	15.220	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.079	-0.047	16.330	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.795	-0.883	17.496	-0.225	-0.225	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.741	-0.831	19.070	0.024	0.024	0.000	0.000	0.000	0.000
82	A	82	PRO	0	0.021	0.008	17.712	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.009	0.010	19.758	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.024	-0.060	23.553	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.021	0.007	20.829	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.034	-0.007	21.005	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.062	-0.032	22.478	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.056	-0.018	23.877	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.011	0.007	23.209	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.745	0.849	19.312	0.173	0.173	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.082	-0.052	16.494	-0.037	-0.037	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.849	0.907	17.934	0.078	0.078	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.030	0.012	17.920	0.012	0.012	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.831	-0.884	18.335	0.018	0.018	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.044	0.012	20.477	0.036	0.036	0.000	0.000	0.000	0.000
96	A	96	ASN	0	0.004	-0.009	23.061	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.010	0.006	24.031	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	98	MET	0	0.068	0.039	23.489	0.005	0.005	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.828	-0.917	26.505	0.113	0.113	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.000	0.003	29.563	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	101	GLN	0	0.009	-0.006	25.398	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.936	0.978	27.742	-0.142	-0.142	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.016	0.005	31.713	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.014	0.012	33.282	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.002	-0.002	33.673	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.043	-0.016	34.608	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.050	0.012	37.674	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.961	0.982	35.863	-0.117	-0.117	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.844	0.922	35.561	-0.108	-0.108	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.051	-0.004	41.198	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)